------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/ncurses-6.2.20200831.txz Installing /packages/All/readline-8.0.4.txz Installing /packages/All/bash-5.0.18_3.txz Installing /packages/All/vim-console-8.2.1558.txz Installing /packages/All/gmake-4.3_2.txz Installing /packages/All/pkgconf-1.7.3,1.txz Installing /packages/All/m4-1.4.18_1,1.txz Installing /packages/All/autoconf-wrapper-20131203.txz Installing /packages/All/perl5-5.32.0.txz Installing /packages/All/autoconf-2.69_3.txz Installing /packages/All/automake-1.16.2.txz SUCCEEDED 00:00:13 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> plumed-2.6.1 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> plumed-2.6.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by plumed-2.6.1 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> plumed-2.6.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by plumed-2.6.1 for building => SHA256 Checksum OK for plumed-plumed2-v2.6.1_GH0.tar.gz. SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> plumed-2.6.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by plumed-2.6.1 for building ===> Extracting for plumed-2.6.1 ===> plumed-2.6.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by plumed-2.6.1 for building => SHA256 Checksum OK for plumed-plumed2-v2.6.1_GH0.tar.gz. Extracted Memory Use: 323.81M SUCCEEDED 00:00:07 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for plumed-2.6.1 ===> Applying ports patches for plumed-2.6.1 from /xports/science/plumed/files /usr/bin/env WRKSRC=/construction/science/plumed/plumed2-2.6.1 REWARNFILE=/construction/science/plumed/reinplace_warnings.txt /xports/Mk/Scripts/sed_checked.sh -e 's,FreeBSD,FreeBSD|DragonFly,g' /construction/science/plumed/plumed2-2.6.1/configure.ac SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> plumed-2.6.1 depends on executable: bash - found ===> plumed-2.6.1 depends on executable: xxd - found ===> plumed-2.6.1 depends on package: gmake>=4.3 - found ===> plumed-2.6.1 depends on package: pkgconf>=1.3.0_1 - found ===> plumed-2.6.1 depends on package: autoconf>=2.69 - found ===> plumed-2.6.1 depends on package: automake>=1.16.1 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> plumed-2.6.1 depends on executable: bash - found ===> plumed-2.6.1 depends on executable: xxd - found ===> plumed-2.6.1 depends on package: gmake>=4.3 - found ===> plumed-2.6.1 depends on package: pkgconf>=1.3.0_1 - found ===> plumed-2.6.1 depends on package: autoconf>=2.69 - found ===> plumed-2.6.1 depends on package: automake>=1.16.1 - found ===> Configuring for plumed-2.6.1 configure: loading site script /xports/Templates/config.site configure: Optional modules are disabled by default checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether c++ accepts -g... yes checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for gfortran... no checking for g95... no checking for xlf95... no checking for f95... no checking for fort... no checking for ifort... no checking for ifc... no checking for efc... no checking for pgfortran... no checking for pgf95... no checking for lf95... no checking for ftn... no checking for nagfor... no checking for xlf90... no checking for f90... no checking for pgf90... no checking for pghpf... no checking for epcf90... no checking for g77... no checking for xlf... no checking for f77... no checking for frt... no checking for pgf77... no checking for cf77... no checking for fort77... no checking for fl32... no checking for af77... no checking whether we are using the GNU Fortran compiler... no checking whether accepts -g... no configure: Initial CXX: c++ configure: Initial CXXFLAGS: -pipe -O2 -fno-strict-aliasing configure: Initial CPPFLAGS: configure: Initial CFLAGS: -pipe -O2 -fno-strict-aliasing configure: Initial LDFLAGS: configure: Initial LIBS: configure: Initial STATIC_LIBS: configure: Initial LD: configure: Initial LDSHARED: c++ configure: Initial SOEXT: checking whether c++ accepts -fPIC... yes checking whether cc accepts -fPIC... yes checking whether c++ accepts -Wall... yes checking whether c++ accepts -pedantic... yes checking whether c++ accepts -std=c++11... yes checking whether c++ declares c++11 support... yes checking whether C++ library supports C++11 exceptions... yes checking whether c++ can generate dependency file with -MM -MF... yes configure: dependency tracking enabled configure: Now we will check compulsory headers and libraries checking how to run the C++ preprocessor... c++ -E checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for dirent.h... (cached) yes checking for readdir... (cached) yes checking whether dgemv can be linked with no library... no checking whether dgemv_ can be linked with no library... no checking for library containing dgemv... no checking for library containing dgemv_... no configure: WARNING: using internal lapack and blas, could be inefficient configure: Now we will check for optional headers and libraries checking libmolfile_plugin.h usability... no checking libmolfile_plugin.h presence... no checking for libmolfile_plugin.h... no configure: WARNING: cannot enable __PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS configure: WARNING: using internal molfile_plugins, which only support dcd/xtc/trr/trj/crd files checking for dlopen in -ldl... yes checking mpi.h usability... no checking mpi.h presence... no checking for mpi.h... no configure: WARNING: cannot enable __PLUMED_HAS_MPI checking for c++ option to support OpenMP... -fopenmp checking regex.h usability... yes checking regex.h presence... yes checking for regex.h... yes checking for library containing regcomp... none required checking for dlfcn.h... (cached) yes checking for library containing dlopen... none required checking RTLD_DEFAULT without extra libs... yes checking for unistd.h... (cached) yes checking for library containing chdir... none required checking subprocess without extra libs... yes checking for unistd.h... (cached) yes checking for library containing getcwd... none required checking execinfo.h usability... yes checking execinfo.h presence... yes checking for execinfo.h... yes checking for library containing backtrace... no configure: WARNING: cannot enable __PLUMED_HAS_EXECINFO checking for zlib.h... (cached) yes checking for library containing gzopen... -lz checking for library containing cblas_dgemv... no configure: WARNING: cannot enable __PLUMED_HAS_GSL checking xdrfile/xdrfile_xtc.h usability... no checking xdrfile/xdrfile_xtc.h presence... no checking for xdrfile/xdrfile_xtc.h... no configure: WARNING: cannot enable __PLUMED_HAS_XDRFILE checking fftw3.h usability... no checking fftw3.h presence... no checking for fftw3.h... no configure: WARNING: cannot enable __PLUMED_HAS_FFTW configure: Release mode, adding -DNDEBUG configure: *** Special settings for dynamic libraries on Linux *** configure: Dynamic library extension is 'so' configure: LDSHARED and LDFLAGS need special flags checking whether LDFLAGS can contain -rdynamic... yes checking whether LDFLAGS can contain -Wl,-Bsymbolic... yes configure: Using LDSHARED='c++ -shared' configure: Using LDFLAGS=' -rdynamic -Wl,-Bsymbolic' checking whether LDSHARED can create dynamic libraries... yes checking for doxygen... no configure: Manuals will not be generated configure: A PDF version of the manual will not be generated checking for xxd... found checking whether a program can be run on this machine... yes configure: PLUMED seems to be configured properly! configure: ************************** checking whether C++ objects can be grouped with ld -r -o... yes checking whether static libraries can be created with ar cr... yes checking whether static-object constructors can be linked from a static archive... yes configure: I will now check if C++ objects can be linked by C/Fortran compilers configure: This is relevant if you want to use plumed patch --static on a non-C++ code checking whether C can link a C++ object... no checking whether C can link a C++ object with library -lstdc++... yes configure: FC compiler not configured checking for pkg-config... /usr/local/bin/pkg-config configure: bash-completion is not installed or it is installed on a different prefix configure: bash completion for plumed will not be installed configure: **** PLUMED will be installed using the following paths: configure: **** prefix: /usr/local configure: **** exec_prefix: ${prefix} configure: **** bindir: ${exec_prefix}/bin configure: **** libdir: ${exec_prefix}/lib configure: **** includedir: ${prefix}/include configure: **** datarootdir: ${prefix}/share configure: **** datadir: ${datarootdir} configure: **** docdir: ${prefix}/share/doc/plumed configure: **** htmldir: ${docdir} configure: **** Executable will be named plumed configure: **** As of PLUMED 2.5, you cannot change paths anymore during "make install" configure: **** Please configure and make clean to change the prefix configure: WARNING: **** Bash completion for plumed will not be installed, please add the following two lines to your bashrc configure: WARNING: **** _plumed() { eval "$(plumed --no-mpi completion 2>/dev/null)";} configure: WARNING: **** complete -F _plumed -o default plumed configure: WARNING: **** PLUMED will NOT be compiled using MPI because MPI have not been found! configure: creating ./config.status config.status: creating Makefile.conf config.status: creating sourceme.sh config.status: creating stamp-h SUCCEEDED 00:00:16 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for plumed-2.6.1 gmake[2]: Entering directory '/construction/science/plumed/plumed2-2.6.1' gmake lib gmake[3]: Entering directory '/construction/science/plumed/plumed2-2.6.1' gmake -C src gmake[4]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src' gmake -C lib gmake[5]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake dirslinks gmake[6]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lib' *** Updating links to used modules in all directories *** gmake ../analysis.links ../asmjit.links ../bias.links ../blas.links ../cltools.links ../colvar.links ../config.links ../core.links ../function.links ../generic.links ../gridtools.links ../isdb.links ../lapack.links ../lepton.links ../main.links ../mapping.links ../molfile.links ../multicolvar.links ../reference.links ../secondarystructure.links ../setup.links ../tools.links ../vatom.links ../vesselbase.links ../wrapper.links gmake[7]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake -C ../analysis links gmake -C ../asmjit links gmake -C ../bias links gmake -C ../blas links gmake -C ../cltools links gmake -C ../colvar links gmake -C ../config links gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/analysis' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/analysis gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/bias' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/bias gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/cltools' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/cltools gmake -C ../core links gmake -C ../function links gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/asmjit' gmake -C ../generic links gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/blas' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/blas gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/config' gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/blas' gmake -C ../gridtools links gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/function' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/function gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/generic' gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/gridtools' gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/colvar' Nothing to do in /construction/science/plumed/plumed2-2.6.1/src/config gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/config' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/gridtools gmake -C ../isdb links Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/generic Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/asmjit gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/core' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/asmjit' gmake -C ../lapack links ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lapack' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/isdb' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/isdb ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/colvar ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/lapack ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/core ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lapack' gmake -C ../lepton links ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lepton' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/lepton ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: 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echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lepton' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake -C ../main links ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/main' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/main ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/main' gmake -C ../mapping links ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/mapping' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/mapping ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/cltools' gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/core' gmake -C ../molfile links ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake -C ../multicolvar links ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/bias' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/molfile' gmake -C ../reference links ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/molfile ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/reference' gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/gridtools' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/reference gmake -C ../secondarystructure links gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/multicolvar' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/multicolvar ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/secondarystructure' gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/molfile' gmake -C ../setup links Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/secondarystructure ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/setup' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/setup ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/function' gmake -C ../tools links ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/tools' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/tools ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/colvar' gmake -C ../vatom links ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/vatom' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/vatom ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/generic' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake -C ../vesselbase links ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/vesselbase' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/vesselbase ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 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line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/tools' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake -C ../wrapper links ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/wrapper' Nothing to do in /construction/science/plumed/plumed2-2.6.1/src/wrapper gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/wrapper' ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/setup' ../maketools/makelinks.sh: line 24: echo: 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../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe ../maketools/makelinks.sh: line 24: echo: write error: Broken pipe gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/isdb' gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/multicolvar' gmake[7]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake[6]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake dirs gmake[6]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lib' *** Compiling all directories *** gmake ../analysis ../asmjit ../bias ../blas ../cltools ../colvar ../config ../core ../function ../generic ../gridtools ../isdb ../lapack ../lepton ../main ../mapping ../molfile ../multicolvar ../reference ../secondarystructure ../setup ../tools ../vatom ../vesselbase ../wrapper gmake[7]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake -C ../analysis obj gmake -C ../asmjit obj gmake -C ../bias obj gmake -C ../blas obj gmake -C ../cltools obj gmake -C ../colvar obj gmake -C ../config obj gmake -C ../core obj gmake -C ../function obj gmake -C ../generic obj gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/function' compiling Combine.cpp gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/analysis' gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/core' compiling Action.cpp gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/generic' compiling Debug.cpp gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/asmjit' compiling AnalysisBase.cpp gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/bias' compiling ABMD.cpp gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/blas' compiling blas.cpp compiling arch.cpp gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/colvar' gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/config' gmake PLUMED_FORCE=yes ConfigInstall.inc Config.inc version.h config.txt gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/config' Updating ConfigInstall.inc gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/cltools' compiling CLTool.cpp compiling Angle.cpp cmp -s ConfigInstall.inc~ ConfigInstall.inc || cp ConfigInstall.inc~ ConfigInstall.inc compiling assembler.cpp rm ConfigInstall.inc~ Updating Config.inc cmp -s Config.inc~ Config.inc || cp Config.inc~ Config.inc rm Config.inc~ compiling codebuilder.cpp Updating version.h Updating config.txt file compiling codecompiler.cpp compiling codeemitter.cpp compiling codeholder.cpp compiling constpool.cpp compiling cpuinfo.cpp compiling func.cpp compiling globals.cpp compiling inst.cpp compiling logging.cpp compiling operand.cpp compiling osutils.cpp gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/config' gmake Config.o ConfigInstall.o compile_options.sh gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/config' cat ../../Makefile.conf | xxd -i > Makefile.conf.xxd Building compile_options.sh, a sourceable bash script with some compilation options compiling Config.cpp compiling regalloc.cpp compiling runtime.cpp compiling string.cpp compiling utils.cpp compiling vmem.cpp compiling x86assembler.cpp compiling x86builder.cpp compiling x86compiler.cpp compiling x86inst.cpp compiling x86instimpl.cpp compiling x86internal.cpp compiling x86logging.cpp compiling x86operand.cpp compiling x86operand_regs.cpp compiling x86regalloc.cpp compiling zone.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/asmjit' compiling ConfigInstall.cpp { ../maketools/make-scripts-options.sh ; cat completion.sh ; }| xxd -i > completion.xxd ../../scripts/selector.sh: line 219: python: command not found compiling Driver.cpp compiling Bias.cpp gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/config' gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/config' compiling ActionAnyorder.cpp compiling Cell.cpp compiling DumpAtoms.cpp compiling Custom.cpp compiling Average.cpp compiling AverageVessel.cpp compiling ActionAtomistic.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/blas' compiling Committor.cpp compiling DriverDouble.cpp compiling BiasValue.cpp compiling Colvar.cpp compiling DriverFloat.cpp ActionAtomistic.cpp: In member function 'void PLMD::ActionAtomistic::requestAtoms(const std::vector&, bool)': ActionAtomistic.cpp:73:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] if(indexes[i].index()>=n) { std::string num; Tools::convert( indexes[i].serial(),num ); error("atom " + num + " out of range"); } ~~~~~~~~~~~~~~~~~~^~~ ActionAtomistic.cpp: In member function 'void PLMD::ActionAtomistic::interpretAtomList(std::vector >&, std::vector&)': ActionAtomistic.cpp:181:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'const int' [-Wsign-compare] for(unsigned i=0; i::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if(dsigmas.size()!=nranks && dsigmas.size()!=1) ~~~~~~~~~~~~~~^~~~~~~~ compiling Manual.cpp compiling EffectiveEnergyDrift.cpp compiling Dipole.cpp compiling Restraint.cpp compiling ReweightBase.cpp compiling OutputColvarFile.cpp compiling ActionWithValue.cpp compiling PdbRenumber.cpp compiling Distance.cpp compiling EndPlumed.cpp compiling ReweightBias.cpp compiling EEFSolv.cpp compiling SimpleMD.cpp compiling OutputPDBFile.cpp compiling FitToTemplate.cpp compiling ActionWithVirtualAtom.cpp compiling ReweightMetad.cpp compiling ReweightTemperaturePressure.cpp compiling Function.cpp compiling ERMSD.cpp compiling Atoms.cpp compiling Energy.cpp Atoms.cpp: In member function 'void PLMD::Atoms::setAtomsGatindex(int*, bool)': Atoms.cpp:391:22: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if( gatindex.size()==natoms ) { ~~~~~~~~~~~~~~~^~~~~~~~ Atoms.cpp:394:22: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits, int>::value_type' {aka 'int'} and 'unsigned int' [-Wsign-compare] if( gatindex[i]!=i ) { shuffledAtoms=1; break; } Atoms.cpp: In member function 'void PLMD::Atoms::setAtomsContiguous(int)': Atoms.cpp:416:21: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if(gatindex.size() CLToolMainMap.inc ../maketools/makecmd enum < CLToolMain.cpp > CLToolMainEnum.inc compiling CLToolRegister.cpp compiling Plumed.cpp compiling Gyration.cpp compiling MultiRMSD.cpp compiling kT.cpp compiling SelectRandomFrames.cpp compiling Stats.cpp compiling PCARMSD.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/bias' compiling PathMSD.cpp Plumed.cpp: In member function 'virtual void PLMD::generic::Plumed::prepare()': Plumed.cpp:324:26: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] bool redo=(index.size()!=n); ~~~~~~~~~~~~^~~ Plumed.cpp: In member function 'virtual void PLMD::generic::Plumed::calculate()': Plumed.cpp:365:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i=0; i&, PLMD::VectorGeneric&, PLMD::TensorGeneric&) [with unsigned int n_ = 3; unsigned int m_ = 3; unsigned int n = 3; unsigned int m = 3]': Gyration.cpp:252:43: required from here core/../../core/tools/../../tools/Tensor.h:557:17: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for(int i=0; i1e-14) break; ~^~ core/../../core/tools/../../tools/Tensor.h:560:9: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] if(j4*comm.Get_size()) { ~~~^~~~~~~~~~~~~~~~~~ Colvar.cpp:103:11: warning: comparison of integer expressions of different signedness: 'const unsigned int' and 'int' [-Wsign-compare] if(ncp>4*comm.Get_size()) { ~~~^~~~~~~~~~~~~~~~~~ DataFetchingObject.cpp: In static member function 'static void PLMD::DataFetchingObject::get_rank(const PLMD::ActionSet&, const string&, const string&, long int*)': DataFetchingObject.cpp:77:10: warning: unused variable 'val' [-Wunused-variable] Value* val = myv->copyOutput( key ); ^~~ DataFetchingObject.cpp: In static member function 'static void PLMD::DataFetchingObject::get_shape(const PLMD::ActionSet&, const string&, const string&, long int*)': DataFetchingObject.cpp:98:10: warning: unused variable 'val' [-Wunused-variable] Value* val = myv->copyOutput( key ); ^~~ compiling Target.cpp compiling PathMSDBase.cpp compiling Print.cpp compiling RandomExchanges.cpp compiling Completion.cpp compiling Read.cpp compiling ResetCell.cpp compiling ExchangePatterns.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/cltools' compiling FlexibleBin.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/analysis' compiling Position.cpp compiling PropertyMap.cpp compiling Puckering.cpp compiling RMSD.cpp compiling Time.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/function' compiling UpdateIf.cpp gmake -C ../gridtools obj gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/gridtools' compiling ActionWithGrid.cpp ../maketools/makecmd map < GREX.cpp > GREXMap.inc compiling ActionWithInputGrid.cpp ../maketools/makecmd enum < GREX.cpp > GREXEnum.inc compiling MDAtoms.cpp compiling ActionWithIntegral.cpp compiling AverageOnGrid.cpp compiling ContourFindingBase.cpp compiling ConvertToFES.cpp gmake -C ../isdb obj gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/isdb' compiling CS2Backbone.cpp compiling WholeMolecules.cpp ../maketools/makecmd map < PlumedMain.cpp > PlumedMainMap.inc ../maketools/makecmd enum < PlumedMain.cpp > PlumedMainEnum.inc compiling PlumedMainInitializer.cpp compiling Caliber.cpp compiling EMMI.cpp compiling FretEfficiency.cpp WholeMolecules.cpp: In constructor 'PLMD::generic::WholeMolecules::WholeMolecules(const PLMD::ActionOptions&)': WholeMolecules.cpp:156:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i=0; i PLMD::isdb::EMMI::read_exp_errors(std::__cxx11::string)': EMMI.cpp:775:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] for(unsigned i=0; i, int>::value_type' {aka 'int'} and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(GMM_d_beta_[i]>=GMM_d_grps_.size()) error("Check Beta values"); Caliber.cpp: In member function 'double PLMD::isdb::Caliber::getSpline(unsigned int)': Caliber.cpp:275:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(tindex+1 >&)': CompiledExpression.cpp:157:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0; i < node.getChildren().size(); i++) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ CompiledExpression.cpp:179:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 1; i < args.size(); i++) ~~^~~~~~~~~~~~~ CompiledExpression.cpp: In member function 'double PLMD::lepton::CompiledExpression::evaluate() const': CompiledExpression.cpp:240:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0; i < variablesToCopy.size(); i++) ~~^~~~~~~~~~~~~~~~~~~~~~~~ CompiledExpression.cpp:245:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int step = 0; step < operation.size(); step++) { ~~~~~^~~~~~~~~~~~~~~~~~ CompiledExpression.cpp:250:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0; i < args.size(); i++) ~~^~~~~~~~~~~~~ CompiledExpression.cpp:236:23: warning: unused variable 'asmjit' [-Wunused-variable] static const bool asmjit=useAsmJit(); ^~~~~~ compiling WrapAround.cpp compiling FindContour.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/colvar' compiling Metainference.cpp compiling ExpressionProgram.cpp compiling Value.cpp gmake -C ../main obj gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/main' compiling main.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/generic' compiling MetainferenceBase.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/main' compiling ExpressionTreeNode.cpp gmake -C ../mapping obj gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/mapping' compiling AdaptivePath.cpp compiling WithCmd.cpp compiling Operation.cpp ExpressionTreeNode.cpp: In constructor 'PLMD::lepton::ExpressionTreeNode::ExpressionTreeNode(PLMD::lepton::Operation*, const std::vector&)': ExpressionTreeNode.cpp:73:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (operation->getNumArguments() != children.size()) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ ExpressionTreeNode.cpp: In constructor 'PLMD::lepton::ExpressionTreeNode::ExpressionTreeNode(PLMD::lepton::Operation*, const PLMD::lepton::ExpressionTreeNode&, const PLMD::lepton::ExpressionTreeNode&)': ExpressionTreeNode.cpp:80:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (operation->getNumArguments() != children.size()) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ ExpressionTreeNode.cpp: In constructor 'PLMD::lepton::ExpressionTreeNode::ExpressionTreeNode(PLMD::lepton::Operation*, const PLMD::lepton::ExpressionTreeNode&)': ExpressionTreeNode.cpp:86:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (operation->getNumArguments() != children.size()) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ ExpressionTreeNode.cpp: In constructor 'PLMD::lepton::ExpressionTreeNode::ExpressionTreeNode(PLMD::lepton::Operation*)': ExpressionTreeNode.cpp:91:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (operation->getNumArguments() != children.size()) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ AdaptivePath.cpp: In constructor 'PLMD::mapping::AdaptivePath::AdaptivePath(const PLMD::ActionOptions&)': AdaptivePath.cpp:154:17: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for(int i=0; i::search(PLMD::Brent1DRootSearch::eng_pointer) [with FCLASS = PLMD::F1dim]': tools/../../tools/Brent1DRootSearch.h:100:57: warning: 'e' may be used uninitialized in this function [-Wmaybe-uninitialized] p=fabs(p); min1=3.0*xm*q-fabs(tol1*q); min2=fabs(e*q); ~^~ compiling GREX.cpp compiling PCAVars.cpp compiling FindContourSurface.cpp compiling Parser.cpp compiling PRE.cpp Parser.cpp: In static member function 'static PLMD::lepton::ParsedExpression PLMD::lepton::Parser::parse(const string&, const std::map, PLMD::lepton::CustomFunction*>&)': Parser.cpp:238:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (pos != tokens.size()) ~~~~^~~~~~~~~~~~~~~~ Parser.cpp:247:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (pos != tokens.size()) ~~~~^~~~~~~~~~~~~~~~ Parser.cpp: In static member function 'static PLMD::lepton::ExpressionTreeNode PLMD::lepton::Parser::parsePrecedence(const std::vector&, int&, const std::map, PLMD::lepton::CustomFunction*>&, const std::map, PLMD::lepton::ExpressionTreeNode>&, int)': Parser.cpp:258:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (pos == tokens.size()) ~~~~^~~~~~~~~~~~~~~~ Parser.cpp:284:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (pos == tokens.size() || tokens[pos].getType() != ParseToken::RightParen) ~~~~^~~~~~~~~~~~~~~~ Parser.cpp:298:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (pos == tokens.size() || tokens[pos].getType() != ParseToken::RightParen) ~~~~^~~~~~~~~~~~~~~~ compiling Path.cpp compiling PlumedMain.cpp compiling RDC.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lepton' compiling FindSphericalContour.cpp compiling FourierTransform.cpp In file included from tools/../../tools/RootFindingBase.h:26, from tools/RootFindingBase.h:1, from ContourFindingBase.h:26, from FindContourSurface.cpp:23: tools/../../tools/Brent1DRootSearch.h: In member function 'double PLMD::Brent1DRootSearch::search(PLMD::Brent1DRootSearch::eng_pointer) [with FCLASS = PLMD::F1dim]': tools/../../tools/Brent1DRootSearch.h:100:57: warning: 'e' may be used uninitialized in this function [-Wmaybe-uninitialized] p=fabs(p); min1=3.0*xm*q-fabs(tol1*q); min2=fabs(e*q); ~^~ compiling PathBase.cpp gmake -C ../molfile obj gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/molfile' compiling crdplugin.cpp compiling dcdplugin.cpp dcdplugin.cpp: In function 'int PLMD::molfile::read_dcdheader(PLMD::molfile::fio_fd, int*, int*, int*, int*, double*, int*, int**, float**, int*, int*)': dcdplugin.cpp:226:57: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] } else if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) { ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ dcdplugin.cpp:239:54: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) { ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ dcdplugin.cpp:257:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] if (input_integer[0] != dcdcordmagic) { ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ dcdplugin.cpp:434:45: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ dcdplugin.cpp:451:45: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ dcdplugin.cpp: In function 'int PLMD::molfile::read_dcdstep(PLMD::molfile::fio_fd, int, float*, float*, float*, float*, int, int, int*, float*, int, int)': dcdplugin.cpp:656:23: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT; ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ dcdplugin.cpp:660:43: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] if ((tmpbuf[2*i]+tmpbuf[2*i+1]) != sizeof(float)*N) return DCD_BADFORMAT; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ dcdplugin.cpp:581:16: warning: variable 'readlen' set but not used [-Wunused-but-set-variable] fio_size_t readlen; /* number of bytes actually read */ ^~~~~~~ In file included from dcdplugin.cpp:92: endianswap.h: At global scope: endianswap.h:136:13: warning: 'void PLMD::molfile::swap2_aligned(void*, long int)' defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ endianswap.h:72:13: warning: 'void PLMD::molfile::swap2_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ In file included from dcdplugin.cpp:83: fastio.h:676:12: warning: 'int PLMD::molfile::fio_write_str(PLMD::molfile::fio_fd, const char*)' defined but not used [-Wunused-function] static int fio_write_str(fio_fd fd, const char *str) { ^~~~~~~~~~~~~ fastio.h:672:12: warning: 'int PLMD::molfile::fio_read_int32(PLMD::molfile::fio_fd, int*)' defined but not used [-Wunused-function] static int fio_read_int32(fio_fd fd, int *i) { ^~~~~~~~~~~~~~ fastio.h:520:19: warning: 'PLMD::molfile::fio_size_t PLMD::molfile::fio_readv(PLMD::molfile::fio_fd, const PLMD::molfile::fio_iovec*, int)' defined but not used [-Wunused-function] static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) { ^~~~~~~~~ compiling PathReparameterization.cpp compiling gromacsplugin.cpp In file included from Gromacs.h:86, from gromacsplugin.cpp:62: endianswap.h:136:13: warning: 'void PLMD::molfile::swap2_aligned(void*, long int)' defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ endianswap.h:105:13: warning: 'void PLMD::molfile::swap8_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ endianswap.h:86:13: warning: 'void PLMD::molfile::swap4_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ endianswap.h:72:13: warning: 'void PLMD::molfile::swap2_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ compiling pdbplugin.cpp In file included from pdbplugin.cpp:64: periodic_table.h:173:12: warning: 'int PLMD::molfile::get_pte_idx(const char*)' defined but not used [-Wunused-function] static int get_pte_idx(const char *label) ^~~~~~~~~~~ compiling GridPrintingBase.cpp In file included from pdbplugin.cpp:63: In function 'void PLMD::molfile::get_pdb_cryst1(const char*, float*, float*, float*, float*, float*, float*)', inlined from 'int PLMD::molfile::read_next_timestep(void*, int, PLMD::molfile::molfile_timestep_t*)' at pdbplugin.cpp:312:23: readpdb.h:160:10: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 80 bytes from a string of length 82 [-Wstringop-truncation] strncpy(tmp, record, PDB_RECORD_LENGTH); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compiling Rescale.cpp In file included from gromacsplugin.cpp:62: Gromacs.h: In function 'int PLMD::molfile::g96_header(PLMD::molfile::md_file*, char*, int, float*)': Gromacs.h:691:32: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 80 bytes from a string of length 500 [-Wstringop-truncation] if (title && titlelen) strncpy(title, buf, titlelen); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ Gromacs.h: In function 'int PLMD::molfile::gro_header(PLMD::molfile::md_file*, char*, int, float*, int*, int)': Gromacs.h:1059:33: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying between 1 and 80 bytes from a string of length 500 [-Wstringop-truncation] if (title && titlelen) strncpy(title, buf, titlelen); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ gromacsplugin.cpp: In function 'void* PLMD::molfile::open_gro_read(const char*, const char*, int*)': gromacsplugin.cpp:138:12: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 80 bytes from a string of length 80 [-Wstringop-truncation] strncpy(gmx->meta->title, mdh.title, 80); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lapack' compiling GridSearch.cpp In file included from gromacsplugin.cpp:62: In function 'int PLMD::molfile::mdio_header(PLMD::molfile::md_file*, PLMD::molfile::md_header*)', inlined from 'void* PLMD::molfile::open_trr_read(const char*, const char*, int*)' at gromacsplugin.cpp:495:20: Gromacs.h:587:10: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 80 bytes from a string of length 80 [-Wstringop-truncation] strncpy(mdh->title, mf->trx->title, MAX_MDIO_TITLE); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from tools/../../tools/RootFindingBase.h:26, from tools/RootFindingBase.h:1, from ContourFindingBase.h:26, from FindSphericalContour.cpp:23: tools/../../tools/Brent1DRootSearch.h: In member function 'double PLMD::Brent1DRootSearch::search(PLMD::Brent1DRootSearch::eng_pointer) [with FCLASS = PLMD::F1dim]': tools/../../tools/Brent1DRootSearch.h:100:57: warning: 'e' may be used uninitialized in this function [-Wmaybe-uninitialized] p=fabs(p); min1=3.0*xm*q-fabs(tol1*q); min2=fabs(e*q); ~^~ PathReparameterization.cpp: In member function 'void PLMD::mapping::PathReparameterization::reparameterizePart(const int&, const int&, const double&, const double&)': PathReparameterization.cpp:72:31: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] for(unsigned i=istart; i= iend+1 ) plumed_merror("path reparameterization error"); ~~~~^~~~~~ PathReparameterization.cpp:103:22: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] else if( cfin==(iend+1) && k>=iend ) { k=iend-1; break; } ~~~~^~~~~~~~~~ PathReparameterization.cpp:104:22: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] else if( cfin==(iend-1) && k<=iend ) { k=iend+1; break; } ~~~~^~~~~~~~~~ PathReparameterization.cpp: In member function 'void PLMD::mapping::PathReparameterization::reparameterize(const int&, const int&, const double&)': PathReparameterization.cpp:141:12: warning: comparison of integer expressions of different signedness: 'const int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if( ifix2<(mypath.size()-1) ) reparameterizePart( ifix2, mypath.size()-1, target, TOL ); ~~~~~^~~~~~~~~~~~~~~~~~ gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/molfile' compiling GridToXYZ.cpp compiling PathTools.cpp compiling PropertyMap.cpp gmake -C ../multicolvar obj gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/multicolvar' compiling ActionVolume.cpp PathTools.cpp: In member function 'virtual int PLMD::mapping::PathTools::main(FILE*, FILE*, PLMD::Communicator&)': PathTools.cpp:268:17: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for(int i=0; i&)': TrigonometricPathVessel.cpp:137:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] if( iclose3<0 || iclose3>=mymap->getFullNumberOfTasks() ) { ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compiling GridVessel.cpp compiling Angles.cpp compiling ZpathVessel.cpp GridVessel.cpp: In member function 'void PLMD::gridtools::GridVessel::getNeighbors(const std::vector&, const std::vector&, unsigned int&, std::vector&) const': GridVessel.cpp:415:23: warning: comparison of integer expressions of different signedness: 'int' and 'const value_type' {aka 'const unsigned int'} [-Wsign-compare] if(!pbc[i] && i0>=nbin[i]) found=false; GridVessel.cpp:417:23: warning: comparison of integer expressions of different signedness: 'int' and 'const value_type' {aka 'const unsigned int'} [-Wsign-compare] if( pbc[i] && i0>=nbin[i]) i0%=nbin[i]; compiling AtomValuePack.cpp compiling Bridge.cpp compiling Selector.cpp gmake -C ../reference obj gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/reference' compiling ArgumentOnlyDistance.cpp compiling HistogramOnGrid.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/core' compiling IntegrateGrid.cpp gmake -C ../secondarystructure obj gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/secondarystructure' compiling AlphaRMSD.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/mapping' compiling BridgedMultiColvarFunction.cpp compiling DRMSD.cpp compiling AntibetaRMSD.cpp compiling Direction.cpp compiling ParabetaRMSD.cpp gmake -C ../setup obj gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/setup' compiling Load.cpp compiling SecondaryStructureRMSD.cpp gmake -C ../tools obj gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/tools' compiling Angle.cpp gmake -C ../vatom obj gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/vatom' compiling ActionWithVirtualAtom.cpp compiling CatomPack.cpp compiling DotProductDistance.cpp GridVessel.cpp: In member function 'unsigned int PLMD::gridtools::GridVessel::getFibonacciIndex(const std::vector&) const': GridVessel.cpp:251:10: warning: 'outind' may be used uninitialized in this function [-Wmaybe-uninitialized] return outind; ^~~~~~ gmake -C ../vesselbase obj gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/vesselbase' compiling ActionWithAveraging.cpp compiling Center.cpp compiling CenterOfMultiColvar.cpp compiling AtomNumber.cpp compiling MolInfo.cpp compiling BiasRepresentation.cpp compiling EuclideanDistance.cpp compiling Brent1DRootSearch.cpp compiling InterpolateGrid.cpp compiling Restart.cpp compiling CoordinationNumbers.cpp compiling Citations.cpp compiling ActionWithInputVessel.cpp compiling FakeFrame.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/isdb' compiling ActionWithVessel.cpp compiling FixedAtom.cpp compiling Communicator.cpp compiling Units.cpp compiling Ghost.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/secondarystructure' compiling AltMin.cpp compiling IntermolecularDRMSD.cpp compiling ConjugateGradient.cpp gmake -C ../wrapper obj gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/wrapper' compiling PlumedStatic.cpp compiling DLLoader.cpp In file included from PlumedStatic.cpp:44: In function 'void* plumed_attempt_dlopen(const char*, int)', inlined from 'plumed plumed_create_dlopen2(const char*, int)' at Plumed.h:2421:49: Plumed.h:2060:33: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] __PLUMED_WRAPPER_STD strncpy(pathcopy,path,strlenpath+1); ^ Plumed.h: In function 'plumed plumed_create_dlopen2(const char*, int)': Plumed.h:2058:43: note: length computed here strlenpath=__PLUMED_WRAPPER_STD strlen(path); ^ compiling AveragingVessel.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/gridtools' compiling Between.cpp compiling IntramolecularDRMSD.cpp compiling Plumed.c gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/vatom' compiling BridgeVessel.cpp In file included from Plumed.c:44: In function 'plumed_attempt_dlopen.part.1', inlined from 'plumed_attempt_dlopen' at Plumed.h:2031:7: Plumed.h:2060:26: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] __PLUMED_WRAPPER_STD strncpy(pathcopy,path,strlenpath+1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Plumed.h: In function 'plumed_attempt_dlopen': Plumed.h:2058:37: note: length computed here strlenpath=__PLUMED_WRAPPER_STD strlen(path); ^~~~~~~~~~~~ compiling DynamicList.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/wrapper' compiling FunctionVessel.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/setup' compiling Density.cpp compiling Highest.cpp compiling MahalanobisDistance.cpp compiling ERMSD.cpp compiling DihedralCorrelation.cpp compiling Exception.cpp compiling FileBase.cpp compiling MetricRegister.cpp compiling Histogram.cpp compiling DistanceFromContour.cpp compiling Distances.cpp compiling DumpMultiColvar.cpp compiling ForwardDecl.cpp compiling LessThan.cpp compiling MultiDomainRMSD.cpp compiling Lowest.cpp compiling Grid.cpp compiling Max.cpp compiling NormalizedEuclideanDistance.cpp compiling OptimalRMSD.cpp compiling Mean.cpp In file included from tools/../../tools/RootFindingBase.h:26, from tools/RootFindingBase.h:1, from DistanceFromContour.cpp:26: tools/../../tools/Brent1DRootSearch.h: In member function 'double PLMD::Brent1DRootSearch::search(PLMD::Brent1DRootSearch::eng_pointer) [with FCLASS = PLMD::F1dim]': tools/../../tools/Brent1DRootSearch.h:100:57: warning: 'e' may be used uninitialized in this function [-Wmaybe-uninitialized] p=fabs(p); min1=3.0*xm*q-fabs(tol1*q); min2=fabs(e*q); ~^~ compiling Min.cpp compiling RMSDBase.cpp compiling Moments.cpp compiling ReferenceArguments.cpp compiling MoreThan.cpp compiling FilterBetween.cpp compiling HistogramBead.cpp compiling FilterLessThan.cpp compiling OrderingVessel.cpp compiling IFile.cpp compiling ReferenceAtoms.cpp In file included from RootFindingBase.h:26, from Grid.cpp:29: Brent1DRootSearch.h: In member function 'double PLMD::Brent1DRootSearch::search(PLMD::Brent1DRootSearch::eng_pointer) [with FCLASS = PLMD::F1dim]': Brent1DRootSearch.h:100:57: warning: 'e' may be used uninitialized in this function [-Wmaybe-uninitialized] p=fabs(p); min1=3.0*xm*q-fabs(tol1*q); min2=fabs(e*q); ~^~ compiling ReferenceConfiguration.cpp compiling FilterMoreThan.cpp compiling ReferenceValuePack.cpp compiling KernelFunctions.cpp compiling Keywords.cpp compiling LatticeReduction.cpp compiling SimpleRMSD.cpp compiling ShortcutVessel.cpp compiling StoreDataVessel.cpp compiling LinkCells.cpp compiling Sum.cpp compiling ValueVessel.cpp compiling SingleDomainRMSD.cpp compiling InPlaneDistances.cpp compiling Vessel.cpp compiling LocalAverage.cpp compiling MultiColvarBase.cpp compiling VesselRegister.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/reference' compiling MultiColvarCombine.cpp compiling MultiColvarDensity.cpp compiling MultiColvarFilter.cpp compiling Log.cpp compiling LoopUnroller.cpp compiling MultiColvarProduct.cpp compiling Matrix.cpp MultiColvarBase.cpp: In member function 'void PLMD::multicolvar::MultiColvarBase::setupActiveTaskSet(std::vector&, const string&)': MultiColvarBase.cpp:743:34: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] if( atom_lab[itask].first==input_code ) active_tasks[ atom_lab[itask].second ]=1; compiling NumberOfLinks.cpp gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/vesselbase' compiling Torsions.cpp compiling MatrixSquareBracketsAccess.cpp compiling Minimise1DBrent.cpp compiling MinimiseBase.cpp compiling VolumeAround.cpp compiling VolumeBetweenContours.cpp compiling MolDataClass.cpp compiling VolumeCavity.cpp compiling VolumeGradientBase.cpp compiling MultiValue.cpp compiling NeighborList.cpp compiling OFile.cpp compiling VolumeInCylinder.cpp compiling VolumeInSphere.cpp compiling VolumeTetrapore.cpp compiling OpenMP.cpp compiling XAngle.cpp compiling XDistances.cpp compiling PDB.cpp compiling XYDistances.cpp compiling Pbc.cpp compiling XYTorsion.cpp compiling PlumedHandle.cpp compiling RMSD.cpp compiling Random.cpp compiling RootFindingBase.cpp In file included from RMSD.h:27, from RMSD.cpp:22: Tensor.h: In instantiation of 'void PLMD::diagMatSym(const PLMD::TensorGeneric&, PLMD::VectorGeneric&, PLMD::TensorGeneric&) [with unsigned int n_ = 4; unsigned int m_ = 4; unsigned int n = 3; unsigned int m = 3]': RMSD.cpp:1028:40: required from here Tensor.h:557:17: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for(int i=0; i1e-14) break; ~^~ Tensor.h:560:9: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] if(j&, PLMD::VectorGeneric&, PLMD::TensorGeneric&) [with unsigned int n_ = 4; unsigned int m_ = 1; unsigned int n = 3; unsigned int m = 3]': RMSD.cpp:1048:50: required from here Tensor.h:557:17: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for(int i=0; i1e-14) break; ~^~ Tensor.h:560:9: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] if(j= digits_size) { ~~~^~~~~~~~~~~~~~ gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/tools' gmake[7]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake[6]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake lib gmake[6]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lib' c++ -pipe -O2 -fno-strict-aliasing -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o ../analysis/DataCollectionObject.o ../analysis/EuclideanDissimilarityMatrix.o ../analysis/FarthestPointSampling.o ../analysis/Histogram.o ../analysis/LandmarkSelectionBase.o ../analysis/LandmarkStaged.o ../analysis/OutputColvarFile.o ../analysis/OutputPDBFile.o ../analysis/PrintDissimilarityMatrix.o ../analysis/ReadAnalysisFrames.o ../analysis/ReadDissimilarityMatrix.o ../analysis/ReselectLandmarks.o ../analysis/SelectRandomFrames.o ../analysis/SelectWithStride.o ../analysis/WhamHistogram.o ../analysis/WhamWeights.o ../asmjit/arch.o ../asmjit/assembler.o ../asmjit/codebuilder.o ../asmjit/codecompiler.o ../asmjit/codeemitter.o ../asmjit/codeholder.o ../asmjit/constpool.o ../asmjit/cpuinfo.o ../asmjit/func.o ../asmjit/globals.o ../asmjit/inst.o ../asmjit/logging.o ../asmjit/operand.o ../asmjit/osutils.o ../asmjit/regalloc.o ../asmjit/runtime.o ../asmjit/string.o ../asmjit/utils.o ../asmjit/vmem.o ../asmjit/x86assembler.o ../asmjit/x86builder.o ../asmjit/x86compiler.o ../asmjit/x86inst.o ../asmjit/x86instimpl.o ../asmjit/x86internal.o ../asmjit/x86logging.o ../asmjit/x86operand.o ../asmjit/x86operand_regs.o ../asmjit/x86regalloc.o ../asmjit/zone.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MaxEnt.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/ReweightBase.o ../bias/ReweightBias.o ../bias/ReweightMetad.o ../bias/ReweightTemperaturePressure.o ../bias/ReweightWham.o ../bias/UWalls.o ../blas/blas.o ../cltools/CLTool.o ../cltools/Completion.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/PdbRenumber.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../cltools/pesmd.o ../colvar/Angle.o ../colvar/Cell.o ../colvar/Colvar.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dimer.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/EEFSolv.o ../colvar/ERMSD.o ../colvar/Energy.o ../colvar/ExtraCV.o ../colvar/Fake.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAnyorder.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionShortcut.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/DataFetchingObject.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/SetupMolInfo.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/LocalEnsemble.o ../function/Piecewise.o ../function/Sort.o ../function/Stats.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/EndPlumed.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/Plumed.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/ResetCell.o ../generic/Time.o ../generic/UpdateIf.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../gridtools/ActionWithGrid.o ../gridtools/ActionWithInputGrid.o ../gridtools/ActionWithIntegral.o ../gridtools/AverageOnGrid.o ../gridtools/ContourFindingBase.o ../gridtools/ConvertToFES.o ../gridtools/DumpCube.o ../gridtools/DumpGrid.o ../gridtools/FindContour.o ../gridtools/FindContourSurface.o ../gridtools/FindSphericalContour.o ../gridtools/FourierTransform.o ../gridtools/GridPrintingBase.o ../gridtools/GridSearch.o ../gridtools/GridToXYZ.o ../gridtools/GridVessel.o ../gridtools/HistogramOnGrid.o ../gridtools/IntegrateGrid.o ../gridtools/InterpolateGrid.o ../isdb/CS2Backbone.o ../isdb/Caliber.o ../isdb/EMMI.o ../isdb/FretEfficiency.o ../isdb/Jcoupling.o ../isdb/Metainference.o ../isdb/MetainferenceBase.o ../isdb/NOE.o ../isdb/PRE.o ../isdb/RDC.o ../isdb/Rescale.o ../isdb/SAXS.o ../isdb/Select.o ../isdb/Selector.o ../lapack/lapack.o ../lepton/CompiledExpression.o ../lepton/ExpressionProgram.o ../lepton/ExpressionTreeNode.o ../lepton/Operation.o ../lepton/ParsedExpression.o ../lepton/Parser.o ../mapping/AdaptivePath.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PathReparameterization.o ../mapping/PathTools.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/TrigonometricPathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CenterOfMultiColvar.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/DistanceFromContour.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarCombine.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarProduct.o ../multicolvar/NumberOfLinks.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeBetweenContours.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeInSphere.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XAngle.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../multicolvar/XYTorsion.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/FakeFrame.o ../reference/IntermolecularDRMSD.o ../reference/IntramolecularDRMSD.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/MolInfo.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/AtomNumber.o ../tools/BiasRepresentation.o ../tools/Brent1DRootSearch.o ../tools/Citations.o ../tools/Communicator.o ../tools/ConjugateGradient.o ../tools/DLLoader.o ../tools/DynamicList.o ../tools/ERMSD.o ../tools/Exception.o ../tools/FileBase.o ../tools/ForwardDecl.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/LoopUnroller.o ../tools/Matrix.o ../tools/MatrixSquareBracketsAccess.o ../tools/Minimise1DBrent.o ../tools/MinimiseBase.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/PDB.o ../tools/Pbc.o ../tools/PlumedHandle.o ../tools/RMSD.o ../tools/Random.o ../tools/RootFindingBase.o ../tools/Stopwatch.o ../tools/Subprocess.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Units.o ../tools/Vector.o ../tools/h36.o ../vatom/ActionWithVirtualAtom.o ../vatom/Center.o ../vatom/FixedAtom.o ../vatom/Ghost.o ../vesselbase/ActionWithAveraging.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/AveragingVessel.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../config/Config.o ../wrapper/PlumedStatic.o -o plumed-static -ldl -lstdc++ -lz -ldl -rdynamic -Wl,-Bsymbolic -fopenmp Building Plumed.inc c++ -shared -o libplumedKernel.so ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o ../analysis/DataCollectionObject.o ../analysis/EuclideanDissimilarityMatrix.o ../analysis/FarthestPointSampling.o ../analysis/Histogram.o ../analysis/LandmarkSelectionBase.o ../analysis/LandmarkStaged.o ../analysis/OutputColvarFile.o ../analysis/OutputPDBFile.o ../analysis/PrintDissimilarityMatrix.o ../analysis/ReadAnalysisFrames.o ../analysis/ReadDissimilarityMatrix.o ../analysis/ReselectLandmarks.o ../analysis/SelectRandomFrames.o ../analysis/SelectWithStride.o ../analysis/WhamHistogram.o ../analysis/WhamWeights.o ../asmjit/arch.o ../asmjit/assembler.o ../asmjit/codebuilder.o ../asmjit/codecompiler.o ../asmjit/codeemitter.o ../asmjit/codeholder.o ../asmjit/constpool.o ../asmjit/cpuinfo.o ../asmjit/func.o ../asmjit/globals.o ../asmjit/inst.o ../asmjit/logging.o ../asmjit/operand.o ../asmjit/osutils.o ../asmjit/regalloc.o ../asmjit/runtime.o ../asmjit/string.o ../asmjit/utils.o ../asmjit/vmem.o ../asmjit/x86assembler.o ../asmjit/x86builder.o ../asmjit/x86compiler.o ../asmjit/x86inst.o ../asmjit/x86instimpl.o ../asmjit/x86internal.o ../asmjit/x86logging.o ../asmjit/x86operand.o ../asmjit/x86operand_regs.o ../asmjit/x86regalloc.o ../asmjit/zone.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MaxEnt.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/ReweightBase.o ../bias/ReweightBias.o ../bias/ReweightMetad.o ../bias/ReweightTemperaturePressure.o ../bias/ReweightWham.o ../bias/UWalls.o ../blas/blas.o ../cltools/CLTool.o ../cltools/Completion.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/PdbRenumber.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../cltools/pesmd.o ../colvar/Angle.o ../colvar/Cell.o ../colvar/Colvar.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dimer.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/EEFSolv.o ../colvar/ERMSD.o ../colvar/Energy.o ../colvar/ExtraCV.o ../colvar/Fake.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAnyorder.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionShortcut.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/DataFetchingObject.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/SetupMolInfo.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/LocalEnsemble.o ../function/Piecewise.o ../function/Sort.o ../function/Stats.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/EndPlumed.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/Plumed.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/ResetCell.o ../generic/Time.o ../generic/UpdateIf.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../gridtools/ActionWithGrid.o ../gridtools/ActionWithInputGrid.o ../gridtools/ActionWithIntegral.o ../gridtools/AverageOnGrid.o ../gridtools/ContourFindingBase.o ../gridtools/ConvertToFES.o ../gridtools/DumpCube.o ../gridtools/DumpGrid.o ../gridtools/FindContour.o ../gridtools/FindContourSurface.o ../gridtools/FindSphericalContour.o ../gridtools/FourierTransform.o ../gridtools/GridPrintingBase.o ../gridtools/GridSearch.o ../gridtools/GridToXYZ.o ../gridtools/GridVessel.o ../gridtools/HistogramOnGrid.o ../gridtools/IntegrateGrid.o ../gridtools/InterpolateGrid.o ../isdb/CS2Backbone.o ../isdb/Caliber.o ../isdb/EMMI.o ../isdb/FretEfficiency.o ../isdb/Jcoupling.o ../isdb/Metainference.o ../isdb/MetainferenceBase.o ../isdb/NOE.o ../isdb/PRE.o ../isdb/RDC.o ../isdb/Rescale.o ../isdb/SAXS.o ../isdb/Select.o ../isdb/Selector.o ../lapack/lapack.o ../lepton/CompiledExpression.o ../lepton/ExpressionProgram.o ../lepton/ExpressionTreeNode.o ../lepton/Operation.o ../lepton/ParsedExpression.o ../lepton/Parser.o ../mapping/AdaptivePath.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PathReparameterization.o ../mapping/PathTools.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/TrigonometricPathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CenterOfMultiColvar.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/DistanceFromContour.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarCombine.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarProduct.o ../multicolvar/NumberOfLinks.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeBetweenContours.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeInSphere.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XAngle.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../multicolvar/XYTorsion.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/FakeFrame.o ../reference/IntermolecularDRMSD.o ../reference/IntramolecularDRMSD.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/MolInfo.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/AtomNumber.o ../tools/BiasRepresentation.o ../tools/Brent1DRootSearch.o ../tools/Citations.o ../tools/Communicator.o ../tools/ConjugateGradient.o ../tools/DLLoader.o ../tools/DynamicList.o ../tools/ERMSD.o ../tools/Exception.o ../tools/FileBase.o ../tools/ForwardDecl.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/LoopUnroller.o ../tools/Matrix.o ../tools/MatrixSquareBracketsAccess.o ../tools/Minimise1DBrent.o ../tools/MinimiseBase.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/PDB.o ../tools/Pbc.o ../tools/PlumedHandle.o ../tools/RMSD.o ../tools/Random.o ../tools/RootFindingBase.o ../tools/Stopwatch.o ../tools/Subprocess.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Units.o ../tools/Vector.o ../tools/h36.o ../vatom/ActionWithVirtualAtom.o ../vatom/Center.o ../vatom/FixedAtom.o ../vatom/Ghost.o ../vesselbase/ActionWithAveraging.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/AveragingVessel.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../config/Config.o -Wl,-soname,"libplumedKernel.so" -lstdc++ -lz -ldl -rdynamic -Wl,-Bsymbolic -fopenmp chmod a+x plumed-patch chmod a+x plumed-config chmod a+x plumed-newcv c++ -pipe -O2 -fno-strict-aliasing -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../wrapper/Plumed.o -o plumed-runtime -ldl ar cr libplumedWrapper.a ../wrapper/Plumed.o chmod a+x plumed-mklib Building Plumed.inc, shared version Building Plumed.cmake Building Plumed.inc, runtime-linking version Building Plumed.inc, static version Building Plumed.cmake, static version chmod a+x plumed-selector Building Plumed.cmake, shared version chmod a+x plumed-partial_tempering chmod a+x plumed-vim2html Building Plumed.cmake, runtime-linking version c++ -shared -o libplumed.so ../wrapper/PlumedStatic.o libplumedKernel.so -Wl,-soname,"libplumed.so" c++ -pipe -O2 -fno-strict-aliasing -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../wrapper/PlumedStatic.o libplumedKernel.so -o plumed -ldl gmake[6]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake install-build gmake[6]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake[6]: ../maketools/purge-d: No such file or directory mkdir -p install/ gmake PLUMED_INSTALL=Install all gmake[7]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake dirslinks gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lib' *** Updating links to used modules in all directories *** gmake ../analysis.links ../asmjit.links ../bias.links ../blas.links ../cltools.links ../colvar.links ../config.links ../core.links ../function.links ../generic.links ../gridtools.links ../isdb.links ../lapack.links ../lepton.links ../main.links ../mapping.links ../molfile.links ../multicolvar.links ../reference.links ../secondarystructure.links ../setup.links ../tools.links ../vatom.links ../vesselbase.links ../wrapper.links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake -C ../analysis links gmake -C ../asmjit links gmake -C ../bias links gmake -C ../blas links gmake -C ../cltools links gmake -C ../colvar links gmake -C ../config links gmake -C ../core links gmake -C ../function links gmake -C ../generic links gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/blas' gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/cltools' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/cltools gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/generic' gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/core' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/core Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/generic gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/analysis' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/analysis gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/colvar' gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/asmjit' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/asmjit gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/function' gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/asmjit' gmake -C ../gridtools links Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/function gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/bias' gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/config' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/blas Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/colvar Nothing to do in /construction/science/plumed/plumed2-2.6.1/src/config gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/config' gmake -C ../isdb links gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/isdb' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/isdb gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/blas' gmake -C ../lapack links gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/gridtools' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/gridtools gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lapack' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/lapack Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/bias gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lapack' gmake -C ../lepton links gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lepton' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/lepton gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lepton' gmake -C ../main links gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/main' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/main gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/main' gmake -C ../mapping links gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/mapping' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/mapping gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/generic' gmake -C ../molfile links gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/molfile' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/molfile gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/molfile' gmake -C ../multicolvar links gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/multicolvar' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/multicolvar gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/colvar' gmake -C ../reference links gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/reference' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/reference gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/cltools' gmake -C ../secondarystructure links gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/secondarystructure' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/secondarystructure gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/core' gmake -C ../setup links gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/setup' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/setup gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/function' gmake -C ../tools links gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/isdb' gmake -C ../vatom links gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/vatom' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/vatom gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/tools' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/tools gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/gridtools' gmake -C ../vesselbase links gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/vesselbase' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/vesselbase gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/analysis' gmake -C ../wrapper links gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/wrapper' Nothing to do in /construction/science/plumed/plumed2-2.6.1/src/wrapper gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/wrapper' gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/tools' gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/bias' gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/reference' gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/mapping' gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/multicolvar' gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/setup' gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/vatom' gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/secondarystructure' gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/vesselbase' gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake dirs gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lib' *** Compiling all directories *** gmake ../analysis ../asmjit ../bias ../blas ../cltools ../colvar ../config ../core ../function ../generic ../gridtools ../isdb ../lapack ../lepton ../main ../mapping ../molfile ../multicolvar ../reference ../secondarystructure ../setup ../tools ../vatom ../vesselbase ../wrapper gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake -C ../analysis obj gmake -C ../asmjit obj gmake -C ../bias obj gmake -C ../blas obj gmake -C ../cltools obj gmake -C ../colvar obj gmake -C ../config obj gmake -C ../core obj gmake -C ../function obj gmake -C ../generic obj gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/asmjit' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/asmjit' gmake -C ../gridtools obj gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/blas' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/blas' gmake -C ../isdb obj gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/cltools' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/cltools' gmake -C ../lapack obj gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/isdb' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/isdb' gmake -C ../lepton obj gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/bias' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/bias' gmake -C ../main obj gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lapack' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lapack' gmake -C ../mapping obj gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/analysis' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/analysis' gmake -C ../molfile obj gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/molfile' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/molfile' gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/main' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/main' gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/mapping' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/mapping' gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/generic' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/generic' gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/function' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/function' gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/core' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/core' gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/config' gmake PLUMED_FORCE=yes ConfigInstall.inc Config.inc version.h config.txt gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lepton' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lepton' gmake[11]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/config' gmake -C ../multicolvar obj gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/colvar' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/colvar' gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/gridtools' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/gridtools' gmake[11]: 'config.txt' is up to date. Updating ConfigInstall.inc gmake -C ../reference obj gmake -C ../secondarystructure obj gmake -C ../setup obj gmake -C ../tools obj gmake -C ../vatom obj gmake -C ../vesselbase obj gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/vatom' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/vatom' gmake -C ../wrapper obj gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/wrapper' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/wrapper' gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/vesselbase' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/vesselbase' gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/setup' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/setup' gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/tools' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/tools' gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/secondarystructure' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/secondarystructure' Updating Config.inc gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/reference' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/reference' Updating version.h cmp -s Config.inc~ Config.inc || cp Config.inc~ Config.inc cmp -s ConfigInstall.inc~ ConfigInstall.inc || cp ConfigInstall.inc~ ConfigInstall.inc rm Config.inc~ rm ConfigInstall.inc~ gmake[11]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/config' gmake Config.o ConfigInstall.o compile_options.sh gmake[11]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/config' gmake[11]: 'Config.o' is up to date. gmake[11]: 'ConfigInstall.o' is up to date. gmake[11]: 'compile_options.sh' is up to date. gmake[11]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/config' gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/config' gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/multicolvar' gmake[10]: Nothing to be done for 'obj'. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/multicolvar' gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake lib gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lib' c++ -pipe -O2 -fno-strict-aliasing -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o ../analysis/DataCollectionObject.o ../analysis/EuclideanDissimilarityMatrix.o ../analysis/FarthestPointSampling.o ../analysis/Histogram.o ../analysis/LandmarkSelectionBase.o ../analysis/LandmarkStaged.o ../analysis/OutputColvarFile.o ../analysis/OutputPDBFile.o ../analysis/PrintDissimilarityMatrix.o ../analysis/ReadAnalysisFrames.o ../analysis/ReadDissimilarityMatrix.o ../analysis/ReselectLandmarks.o ../analysis/SelectRandomFrames.o ../analysis/SelectWithStride.o ../analysis/WhamHistogram.o ../analysis/WhamWeights.o ../asmjit/arch.o ../asmjit/assembler.o ../asmjit/codebuilder.o ../asmjit/codecompiler.o ../asmjit/codeemitter.o ../asmjit/codeholder.o ../asmjit/constpool.o ../asmjit/cpuinfo.o ../asmjit/func.o ../asmjit/globals.o ../asmjit/inst.o ../asmjit/logging.o ../asmjit/operand.o ../asmjit/osutils.o ../asmjit/regalloc.o ../asmjit/runtime.o ../asmjit/string.o ../asmjit/utils.o ../asmjit/vmem.o ../asmjit/x86assembler.o ../asmjit/x86builder.o ../asmjit/x86compiler.o ../asmjit/x86inst.o ../asmjit/x86instimpl.o ../asmjit/x86internal.o ../asmjit/x86logging.o ../asmjit/x86operand.o ../asmjit/x86operand_regs.o ../asmjit/x86regalloc.o ../asmjit/zone.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MaxEnt.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/ReweightBase.o ../bias/ReweightBias.o ../bias/ReweightMetad.o ../bias/ReweightTemperaturePressure.o ../bias/ReweightWham.o ../bias/UWalls.o ../blas/blas.o ../cltools/CLTool.o ../cltools/Completion.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/PdbRenumber.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../cltools/pesmd.o ../colvar/Angle.o ../colvar/Cell.o ../colvar/Colvar.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dimer.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/EEFSolv.o ../colvar/ERMSD.o ../colvar/Energy.o ../colvar/ExtraCV.o ../colvar/Fake.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAnyorder.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionShortcut.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/DataFetchingObject.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/SetupMolInfo.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/LocalEnsemble.o ../function/Piecewise.o ../function/Sort.o ../function/Stats.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/EndPlumed.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/Plumed.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/ResetCell.o ../generic/Time.o ../generic/UpdateIf.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../gridtools/ActionWithGrid.o ../gridtools/ActionWithInputGrid.o ../gridtools/ActionWithIntegral.o ../gridtools/AverageOnGrid.o ../gridtools/ContourFindingBase.o ../gridtools/ConvertToFES.o ../gridtools/DumpCube.o ../gridtools/DumpGrid.o ../gridtools/FindContour.o ../gridtools/FindContourSurface.o ../gridtools/FindSphericalContour.o ../gridtools/FourierTransform.o ../gridtools/GridPrintingBase.o ../gridtools/GridSearch.o ../gridtools/GridToXYZ.o ../gridtools/GridVessel.o ../gridtools/HistogramOnGrid.o ../gridtools/IntegrateGrid.o ../gridtools/InterpolateGrid.o ../isdb/CS2Backbone.o ../isdb/Caliber.o ../isdb/EMMI.o ../isdb/FretEfficiency.o ../isdb/Jcoupling.o ../isdb/Metainference.o ../isdb/MetainferenceBase.o ../isdb/NOE.o ../isdb/PRE.o ../isdb/RDC.o ../isdb/Rescale.o ../isdb/SAXS.o ../isdb/Select.o ../isdb/Selector.o ../lapack/lapack.o ../lepton/CompiledExpression.o ../lepton/ExpressionProgram.o ../lepton/ExpressionTreeNode.o ../lepton/Operation.o ../lepton/ParsedExpression.o ../lepton/Parser.o ../mapping/AdaptivePath.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PathReparameterization.o ../mapping/PathTools.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/TrigonometricPathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CenterOfMultiColvar.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/DistanceFromContour.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarCombine.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarProduct.o ../multicolvar/NumberOfLinks.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeBetweenContours.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeInSphere.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XAngle.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../multicolvar/XYTorsion.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/FakeFrame.o ../reference/IntermolecularDRMSD.o ../reference/IntramolecularDRMSD.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/MolInfo.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/AtomNumber.o ../tools/BiasRepresentation.o ../tools/Brent1DRootSearch.o ../tools/Citations.o ../tools/Communicator.o ../tools/ConjugateGradient.o ../tools/DLLoader.o ../tools/DynamicList.o ../tools/ERMSD.o ../tools/Exception.o ../tools/FileBase.o ../tools/ForwardDecl.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/LoopUnroller.o ../tools/Matrix.o ../tools/MatrixSquareBracketsAccess.o ../tools/Minimise1DBrent.o ../tools/MinimiseBase.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/PDB.o ../tools/Pbc.o ../tools/PlumedHandle.o ../tools/RMSD.o ../tools/Random.o ../tools/RootFindingBase.o ../tools/Stopwatch.o ../tools/Subprocess.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Units.o ../tools/Vector.o ../tools/h36.o ../vatom/ActionWithVirtualAtom.o ../vatom/Center.o ../vatom/FixedAtom.o ../vatom/Ghost.o ../vesselbase/ActionWithAveraging.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/AveragingVessel.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../config/ConfigInstall.o ../wrapper/PlumedStatic.o -o install/plumed-static -ldl -lstdc++ -lz -ldl -rdynamic -Wl,-Bsymbolic -fopenmp mkdir -p install c++ -shared -o install/libplumedKernel.so ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o ../analysis/DataCollectionObject.o ../analysis/EuclideanDissimilarityMatrix.o ../analysis/FarthestPointSampling.o ../analysis/Histogram.o ../analysis/LandmarkSelectionBase.o ../analysis/LandmarkStaged.o ../analysis/OutputColvarFile.o ../analysis/OutputPDBFile.o ../analysis/PrintDissimilarityMatrix.o ../analysis/ReadAnalysisFrames.o ../analysis/ReadDissimilarityMatrix.o ../analysis/ReselectLandmarks.o ../analysis/SelectRandomFrames.o ../analysis/SelectWithStride.o ../analysis/WhamHistogram.o ../analysis/WhamWeights.o ../asmjit/arch.o ../asmjit/assembler.o ../asmjit/codebuilder.o ../asmjit/codecompiler.o ../asmjit/codeemitter.o ../asmjit/codeholder.o ../asmjit/constpool.o ../asmjit/cpuinfo.o ../asmjit/func.o ../asmjit/globals.o ../asmjit/inst.o ../asmjit/logging.o ../asmjit/operand.o ../asmjit/osutils.o ../asmjit/regalloc.o ../asmjit/runtime.o ../asmjit/string.o ../asmjit/utils.o ../asmjit/vmem.o ../asmjit/x86assembler.o ../asmjit/x86builder.o ../asmjit/x86compiler.o ../asmjit/x86inst.o ../asmjit/x86instimpl.o ../asmjit/x86internal.o ../asmjit/x86logging.o ../asmjit/x86operand.o ../asmjit/x86operand_regs.o ../asmjit/x86regalloc.o ../asmjit/zone.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MaxEnt.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/ReweightBase.o ../bias/ReweightBias.o ../bias/ReweightMetad.o ../bias/ReweightTemperaturePressure.o ../bias/ReweightWham.o ../bias/UWalls.o ../blas/blas.o ../cltools/CLTool.o ../cltools/Completion.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/PdbRenumber.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../cltools/pesmd.o ../colvar/Angle.o ../colvar/Cell.o ../colvar/Colvar.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dimer.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/EEFSolv.o ../colvar/ERMSD.o ../colvar/Energy.o ../colvar/ExtraCV.o ../colvar/Fake.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAnyorder.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionShortcut.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/DataFetchingObject.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/SetupMolInfo.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/LocalEnsemble.o ../function/Piecewise.o ../function/Sort.o ../function/Stats.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/EndPlumed.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/Plumed.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/ResetCell.o ../generic/Time.o ../generic/UpdateIf.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../gridtools/ActionWithGrid.o ../gridtools/ActionWithInputGrid.o ../gridtools/ActionWithIntegral.o ../gridtools/AverageOnGrid.o ../gridtools/ContourFindingBase.o ../gridtools/ConvertToFES.o ../gridtools/DumpCube.o ../gridtools/DumpGrid.o ../gridtools/FindContour.o ../gridtools/FindContourSurface.o ../gridtools/FindSphericalContour.o ../gridtools/FourierTransform.o ../gridtools/GridPrintingBase.o ../gridtools/GridSearch.o ../gridtools/GridToXYZ.o ../gridtools/GridVessel.o ../gridtools/HistogramOnGrid.o ../gridtools/IntegrateGrid.o ../gridtools/InterpolateGrid.o ../isdb/CS2Backbone.o ../isdb/Caliber.o ../isdb/EMMI.o ../isdb/FretEfficiency.o ../isdb/Jcoupling.o ../isdb/Metainference.o ../isdb/MetainferenceBase.o ../isdb/NOE.o ../isdb/PRE.o ../isdb/RDC.o ../isdb/Rescale.o ../isdb/SAXS.o ../isdb/Select.o ../isdb/Selector.o ../lapack/lapack.o ../lepton/CompiledExpression.o ../lepton/ExpressionProgram.o ../lepton/ExpressionTreeNode.o ../lepton/Operation.o ../lepton/ParsedExpression.o ../lepton/Parser.o ../mapping/AdaptivePath.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PathReparameterization.o ../mapping/PathTools.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/TrigonometricPathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CenterOfMultiColvar.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/DistanceFromContour.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarCombine.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarProduct.o ../multicolvar/NumberOfLinks.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeBetweenContours.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeInSphere.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XAngle.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../multicolvar/XYTorsion.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/FakeFrame.o ../reference/IntermolecularDRMSD.o ../reference/IntramolecularDRMSD.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/MolInfo.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/AtomNumber.o ../tools/BiasRepresentation.o ../tools/Brent1DRootSearch.o ../tools/Citations.o ../tools/Communicator.o ../tools/ConjugateGradient.o ../tools/DLLoader.o ../tools/DynamicList.o ../tools/ERMSD.o ../tools/Exception.o ../tools/FileBase.o ../tools/ForwardDecl.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/LoopUnroller.o ../tools/Matrix.o ../tools/MatrixSquareBracketsAccess.o ../tools/Minimise1DBrent.o ../tools/MinimiseBase.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/PDB.o ../tools/Pbc.o ../tools/PlumedHandle.o ../tools/RMSD.o ../tools/Random.o ../tools/RootFindingBase.o ../tools/Stopwatch.o ../tools/Subprocess.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Units.o ../tools/Vector.o ../tools/h36.o ../vatom/ActionWithVirtualAtom.o ../vatom/Center.o ../vatom/FixedAtom.o ../vatom/Ghost.o ../vesselbase/ActionWithAveraging.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/AveragingVessel.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../config/ConfigInstall.o -Wl,-soname,"libplumedKernel.so" -lstdc++ -lz -ldl -rdynamic -Wl,-Bsymbolic -fopenmp Building Plumed.inc chmod a+x install/plumed-vim2html chmod a+x install/plumed-patch c++ -pipe -O2 -fno-strict-aliasing -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../wrapper/Plumed.o -o install/plumed-runtime -ldl mkdir -p install chmod a+x install/plumed-newcv ar cr install/libplumedWrapper.a ../wrapper/Plumed.o chmod a+x install/plumed-mklib Building Plumed.inc, runtime-linking version Building Plumed.inc, shared version chmod a+x install/plumed-partial_tempering Building Plumed.inc, static version Building Plumed.cmake chmod a+x install/plumed-selector Building Plumed.cmake, static version Building Plumed.cmake, runtime-linking version chmod a+x install/plumed-config Building Plumed.cmake, shared version mkdir -p install c++ -pipe -O2 -fno-strict-aliasing -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../wrapper/PlumedStatic.o install/libplumedKernel.so -o install/plumed -ldl c++ -shared -o install/libplumed.so ../wrapper/PlumedStatic.o install/libplumedKernel.so -Wl,-soname,"libplumed.so" gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake[7]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake PLUMED_INSTALL=Install install/kernel.o gmake[7]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lib' ld -r -o install/kernel.o ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o ../analysis/DataCollectionObject.o ../analysis/EuclideanDissimilarityMatrix.o ../analysis/FarthestPointSampling.o ../analysis/Histogram.o ../analysis/LandmarkSelectionBase.o ../analysis/LandmarkStaged.o ../analysis/OutputColvarFile.o ../analysis/OutputPDBFile.o ../analysis/PrintDissimilarityMatrix.o ../analysis/ReadAnalysisFrames.o ../analysis/ReadDissimilarityMatrix.o ../analysis/ReselectLandmarks.o ../analysis/SelectRandomFrames.o ../analysis/SelectWithStride.o ../analysis/WhamHistogram.o ../analysis/WhamWeights.o ../asmjit/arch.o ../asmjit/assembler.o ../asmjit/codebuilder.o ../asmjit/codecompiler.o ../asmjit/codeemitter.o ../asmjit/codeholder.o ../asmjit/constpool.o ../asmjit/cpuinfo.o ../asmjit/func.o ../asmjit/globals.o ../asmjit/inst.o ../asmjit/logging.o ../asmjit/operand.o ../asmjit/osutils.o ../asmjit/regalloc.o ../asmjit/runtime.o ../asmjit/string.o ../asmjit/utils.o ../asmjit/vmem.o ../asmjit/x86assembler.o ../asmjit/x86builder.o ../asmjit/x86compiler.o ../asmjit/x86inst.o ../asmjit/x86instimpl.o ../asmjit/x86internal.o ../asmjit/x86logging.o ../asmjit/x86operand.o ../asmjit/x86operand_regs.o ../asmjit/x86regalloc.o ../asmjit/zone.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MaxEnt.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/ReweightBase.o ../bias/ReweightBias.o ../bias/ReweightMetad.o ../bias/ReweightTemperaturePressure.o ../bias/ReweightWham.o ../bias/UWalls.o ../blas/blas.o ../cltools/CLTool.o ../cltools/Completion.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/PdbRenumber.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../cltools/pesmd.o ../colvar/Angle.o ../colvar/Cell.o ../colvar/Colvar.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dimer.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/EEFSolv.o ../colvar/ERMSD.o ../colvar/Energy.o ../colvar/ExtraCV.o ../colvar/Fake.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAnyorder.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionShortcut.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/DataFetchingObject.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/SetupMolInfo.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/LocalEnsemble.o ../function/Piecewise.o ../function/Sort.o ../function/Stats.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/EndPlumed.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/Plumed.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/ResetCell.o ../generic/Time.o ../generic/UpdateIf.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../gridtools/ActionWithGrid.o ../gridtools/ActionWithInputGrid.o ../gridtools/ActionWithIntegral.o ../gridtools/AverageOnGrid.o ../gridtools/ContourFindingBase.o ../gridtools/ConvertToFES.o ../gridtools/DumpCube.o ../gridtools/DumpGrid.o ../gridtools/FindContour.o ../gridtools/FindContourSurface.o ../gridtools/FindSphericalContour.o ../gridtools/FourierTransform.o ../gridtools/GridPrintingBase.o ../gridtools/GridSearch.o ../gridtools/GridToXYZ.o ../gridtools/GridVessel.o ../gridtools/HistogramOnGrid.o ../gridtools/IntegrateGrid.o ../gridtools/InterpolateGrid.o ../isdb/CS2Backbone.o ../isdb/Caliber.o ../isdb/EMMI.o ../isdb/FretEfficiency.o ../isdb/Jcoupling.o ../isdb/Metainference.o ../isdb/MetainferenceBase.o ../isdb/NOE.o ../isdb/PRE.o ../isdb/RDC.o ../isdb/Rescale.o ../isdb/SAXS.o ../isdb/Select.o ../isdb/Selector.o ../lapack/lapack.o ../lepton/CompiledExpression.o ../lepton/ExpressionProgram.o ../lepton/ExpressionTreeNode.o ../lepton/Operation.o ../lepton/ParsedExpression.o ../lepton/Parser.o ../mapping/AdaptivePath.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PathReparameterization.o ../mapping/PathTools.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/TrigonometricPathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CenterOfMultiColvar.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/DistanceFromContour.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarCombine.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarProduct.o ../multicolvar/NumberOfLinks.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeBetweenContours.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeInSphere.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XAngle.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../multicolvar/XYTorsion.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/FakeFrame.o ../reference/IntermolecularDRMSD.o ../reference/IntramolecularDRMSD.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/MolInfo.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/AtomNumber.o ../tools/BiasRepresentation.o ../tools/Brent1DRootSearch.o ../tools/Citations.o ../tools/Communicator.o ../tools/ConjugateGradient.o ../tools/DLLoader.o ../tools/DynamicList.o ../tools/ERMSD.o ../tools/Exception.o ../tools/FileBase.o ../tools/ForwardDecl.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/LoopUnroller.o ../tools/Matrix.o ../tools/MatrixSquareBracketsAccess.o ../tools/Minimise1DBrent.o ../tools/MinimiseBase.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/PDB.o ../tools/Pbc.o ../tools/PlumedHandle.o ../tools/RMSD.o ../tools/Random.o ../tools/RootFindingBase.o ../tools/Stopwatch.o ../tools/Subprocess.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Units.o ../tools/Vector.o ../tools/h36.o ../vatom/ActionWithVirtualAtom.o ../vatom/Center.o ../vatom/FixedAtom.o ../vatom/Ghost.o ../vesselbase/ActionWithAveraging.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/AveragingVessel.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../config/ConfigInstall.o gmake[7]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake PLUMED_INSTALL=Install install/libplumed.a gmake[7]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lib' rm -f install/libplumed.a ar cr install/libplumed.a install/kernel.o ../wrapper/PlumedStatic.o gmake[7]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake[6]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake[5]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake[4]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src' gmake[3]: Leaving directory '/construction/science/plumed/plumed2-2.6.1' gmake -C vim gmake[3]: Entering directory '/construction/science/plumed/plumed2-2.6.1/vim' ./vimsyntax.sh gmake[3]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/vim' gmake -C python gmake[3]: Entering directory '/construction/science/plumed/plumed2-2.6.1/python' Python support was not configure gmake[3]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/python' gmake[2]: Leaving directory '/construction/science/plumed/plumed2-2.6.1' SUCCEEDED 00:05:23 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> plumed-2.6.1 depends on executable: bash - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for plumed-2.6.1 ===> plumed-2.6.1 depends on executable: bash - found ===> Generating temporary packing list gmake[2]: Entering directory '/construction/science/plumed/plumed2-2.6.1' gmake -C src install gmake[3]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src' gmake -C lib install gmake[4]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lib' cd ../config ; gmake gmake[5]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/config' gmake PLUMED_FORCE=yes ConfigInstall.inc Config.inc version.h config.txt gmake[6]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/config' Updating ConfigInstall.inc cmp -s ConfigInstall.inc~ ConfigInstall.inc || cp ConfigInstall.inc~ ConfigInstall.inc rm ConfigInstall.inc~ Updating Config.inc cmp -s Config.inc~ Config.inc || cp Config.inc~ Config.inc rm Config.inc~ Updating version.h gmake[6]: 'config.txt' is up to date. gmake[6]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/config' gmake Config.o ConfigInstall.o compile_options.sh gmake[6]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/config' gmake[6]: 'Config.o' is up to date. gmake[6]: 'ConfigInstall.o' is up to date. gmake[6]: 'compile_options.sh' is up to date. gmake[6]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/config' gmake[5]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/config' # gmake uninstall mkdir -p "/construction/science/plumed/stage/usr/local/bin" mkdir -p "/construction/science/plumed/stage/usr/local/lib" mkdir -p "/construction/science/plumed/stage/usr/local/lib/pkgconfig" mkdir -p "/construction/science/plumed/stage/usr/local/include/plumed" mkdir -p "/construction/science/plumed/stage/usr/local/lib/plumed/obj" mkdir -p "/construction/science/plumed/stage/usr/local/lib/plumed/src/lib" mkdir -p "/construction/science/plumed/stage/usr/local/lib/plumed/src/config" mkdir -p "/construction/science/plumed/stage/usr/local/lib/plumed/src/colvar" gmake install-build gmake[5]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake[5]: ../maketools/purge-d: No such file or directory mkdir -p install/ gmake PLUMED_INSTALL=Install all gmake[6]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake dirslinks gmake[7]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lib' *** Updating links to used modules in all directories *** gmake ../analysis.links ../asmjit.links ../bias.links ../blas.links ../cltools.links ../colvar.links ../config.links ../core.links ../function.links ../generic.links ../gridtools.links ../isdb.links ../lapack.links ../lepton.links ../main.links ../mapping.links ../molfile.links ../multicolvar.links ../reference.links ../secondarystructure.links ../setup.links ../tools.links ../vatom.links ../vesselbase.links ../wrapper.links gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake -C ../analysis links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/analysis' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/analysis gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/analysis' gmake -C ../asmjit links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/asmjit' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/asmjit gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/asmjit' gmake -C ../bias links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/bias' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/bias gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/bias' gmake -C ../blas links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/blas' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/blas gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/blas' gmake -C ../cltools links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/cltools' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/cltools gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/cltools' gmake -C ../colvar links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/colvar' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/colvar gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/colvar' gmake -C ../config links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/config' Nothing to do in /construction/science/plumed/plumed2-2.6.1/src/config gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/config' gmake -C ../core links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/core' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/core gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/core' gmake -C ../function links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/function' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/function gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/function' gmake -C ../generic links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/generic' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/generic gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/generic' gmake -C ../gridtools links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/gridtools' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/gridtools gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/gridtools' gmake -C ../isdb links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/isdb' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/isdb gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/isdb' gmake -C ../lapack links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lapack' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/lapack gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lapack' gmake -C ../lepton links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lepton' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/lepton gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lepton' gmake -C ../main links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/main' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/main gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/main' gmake -C ../mapping links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/mapping' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/mapping gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/mapping' gmake -C ../molfile links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/molfile' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/molfile gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/molfile' gmake -C ../multicolvar links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/multicolvar' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/multicolvar gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/multicolvar' gmake -C ../reference links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/reference' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/reference gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/reference' gmake -C ../secondarystructure links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/secondarystructure' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/secondarystructure gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/secondarystructure' gmake -C ../setup links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/setup' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/setup gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/setup' gmake -C ../tools links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/tools' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/tools gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/tools' gmake -C ../vatom links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/vatom' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/vatom gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/vatom' gmake -C ../vesselbase links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/vesselbase' Verify modules and create links in /construction/science/plumed/plumed2-2.6.1/src/vesselbase gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/vesselbase' gmake -C ../wrapper links gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/wrapper' Nothing to do in /construction/science/plumed/plumed2-2.6.1/src/wrapper gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/wrapper' gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake[7]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake dirs gmake[7]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lib' *** Compiling all directories *** gmake ../analysis ../asmjit ../bias ../blas ../cltools ../colvar ../config ../core ../function ../generic ../gridtools ../isdb ../lapack ../lepton ../main ../mapping ../molfile ../multicolvar ../reference ../secondarystructure ../setup ../tools ../vatom ../vesselbase ../wrapper gmake[8]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake -C ../analysis obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/analysis' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/analysis' gmake -C ../asmjit obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/asmjit' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/asmjit' gmake -C ../bias obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/bias' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/bias' gmake -C ../blas obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/blas' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/blas' gmake -C ../cltools obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/cltools' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/cltools' gmake -C ../colvar obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/colvar' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/colvar' gmake -C ../config obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/config' gmake PLUMED_FORCE=yes ConfigInstall.inc Config.inc version.h config.txt gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/config' Updating ConfigInstall.inc cmp -s ConfigInstall.inc~ ConfigInstall.inc || cp ConfigInstall.inc~ ConfigInstall.inc rm ConfigInstall.inc~ Updating Config.inc cmp -s Config.inc~ Config.inc || cp Config.inc~ Config.inc rm Config.inc~ Updating version.h gmake[10]: 'config.txt' is up to date. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/config' gmake Config.o ConfigInstall.o compile_options.sh gmake[10]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/config' gmake[10]: 'Config.o' is up to date. gmake[10]: 'ConfigInstall.o' is up to date. gmake[10]: 'compile_options.sh' is up to date. gmake[10]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/config' gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/config' gmake -C ../core obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/core' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/core' gmake -C ../function obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/function' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/function' gmake -C ../generic obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/generic' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/generic' gmake -C ../gridtools obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/gridtools' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/gridtools' gmake -C ../isdb obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/isdb' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/isdb' gmake -C ../lapack obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lapack' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lapack' gmake -C ../lepton obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lepton' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lepton' gmake -C ../main obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/main' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/main' gmake -C ../mapping obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/mapping' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/mapping' gmake -C ../molfile obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/molfile' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/molfile' gmake -C ../multicolvar obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/multicolvar' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/multicolvar' gmake -C ../reference obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/reference' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/reference' gmake -C ../secondarystructure obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/secondarystructure' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/secondarystructure' gmake -C ../setup obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/setup' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/setup' gmake -C ../tools obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/tools' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/tools' gmake -C ../vatom obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/vatom' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/vatom' gmake -C ../vesselbase obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/vesselbase' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/vesselbase' gmake -C ../wrapper obj gmake[9]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/wrapper' gmake[9]: Nothing to be done for 'obj'. gmake[9]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/wrapper' gmake[8]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake[7]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake lib gmake[7]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lib' Building Plumed.inc Building Plumed.inc, static version Building Plumed.cmake Building Plumed.cmake, static version chmod a+x install/plumed-config chmod a+x install/plumed-mklib chmod a+x install/plumed-newcv chmod a+x install/plumed-partial_tempering chmod a+x install/plumed-patch chmod a+x install/plumed-selector chmod a+x install/plumed-vim2html Building Plumed.inc, runtime-linking version Building Plumed.inc, shared version Building Plumed.cmake, runtime-linking version Building Plumed.cmake, shared version gmake[7]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake[6]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake PLUMED_INSTALL=Install install/kernel.o gmake[6]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake[6]: 'install/kernel.o' is up to date. gmake[6]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake PLUMED_INSTALL=Install install/libplumed.a gmake[6]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake[6]: 'install/libplumed.a' is up to date. gmake[6]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake[5]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake install-html gmake[5]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lib' if test -d ../../user-doc/html ; then mkdir -p "/construction/science/plumed/stage/usr/local/share/doc/plumed" && cd ../../ && tar cf - user-doc/html | tar xf - -C "/construction/science/plumed/stage/usr/local/share/doc/plumed/" ; fi if test -d ../../developer-doc/html ; then mkdir -p "/construction/science/plumed/stage/usr/local/share/doc/plumed" && cd ../../ && tar cf - developer-doc/html | tar xf - -C "/construction/science/plumed/stage/usr/local/share/doc/plumed/" ; fi if test -d ../../developer-doc/coverage ; then mkdir -p "/construction/science/plumed/stage/usr/local/share/doc/plumed" && cd ../../ && tar cf - developer-doc/coverage | tar xf - -C "/construction/science/plumed/stage/usr/local/share/doc/plumed/" ; fi if test -f ../../user-doc/manual.pdf ; then mkdir -p "/construction/science/plumed/stage/usr/local/share/doc/plumed/user-doc" && cp ../../user-doc/manual.pdf "/construction/science/plumed/stage/usr/local/share/doc/plumed/user-doc/" ; fi gmake[5]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lib' cd ../../ ; tar cf - patches scripts | tar xf - -C "/construction/science/plumed/stage/usr/local/lib/plumed/" cp ../colvar/Template.cpp "/construction/science/plumed/stage/usr/local/lib/plumed/src/colvar/" grep -v "^link_uninstalled=" ../config/compile_options.sh > "/construction/science/plumed/stage/usr/local/lib/plumed/src/config/compile_options.sh" cp ../config/config.txt "/construction/science/plumed/stage/usr/local/lib/plumed/src/config/config.txt" cp install/libplumed.a "/construction/science/plumed/stage/usr/local/lib/" gmake install-headers gmake[5]: Entering directory '/construction/science/plumed/plumed2-2.6.1/src/lib' bash ../maketools/install.headers "/construction/science/plumed/stage/usr/local/include/plumed/" analysis asmjit bias blas cltools colvar config core function generic gridtools isdb lapack lepton main mapping molfile multicolvar reference secondarystructure setup tools vatom vesselbase wrapper gmake[5]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lib' cp install/"plumed" "/construction/science/plumed/stage/usr/local/bin/" cp install/plumed-patch "/construction/science/plumed/stage/usr/local/bin/plumed-patch" cp install/plumed-config "/construction/science/plumed/stage/usr/local/bin/plumed-config" cp install/Plumed.cmake* "/construction/science/plumed/stage/usr/local/lib/plumed/src/lib/" cp install/Plumed.inc* "/construction/science/plumed/stage/usr/local/lib/plumed/src/lib/" for file in config mklib newcv partial_tempering patch selector vim2html ; do cp install/plumed-$file "/construction/science/plumed/stage/usr/local/lib/plumed/plumed-$file" ; done cp install/lib"plumed".so "/construction/science/plumed/stage/usr/local/lib/" cp install/lib"plumed"Kernel.so "/construction/science/plumed/stage/usr/local/lib/" if test -e install/"plumed"-runtime ; then cp install/"plumed"-runtime "/construction/science/plumed/stage/usr/local/lib/plumed/plumed-runtime" ; fi cp install/libplumedWrapper.a "/construction/science/plumed/stage/usr/local/lib/" cp install/modulefile "/construction/science/plumed/stage/usr/local/lib/plumed/modulefile" cp install/pkgconfig "/construction/science/plumed/stage/usr/local/lib/pkgconfig/plumed.pc" cp install/pkgconfigWrapper "/construction/science/plumed/stage/usr/local/lib/pkgconfig/plumedWrapper.pc" cp install/pkgconfigInternals "/construction/science/plumed/stage/usr/local/lib/pkgconfig/plumedInternals.pc" if test -d ../../vim/syntax ; then mkdir -p "/construction/science/plumed/stage/usr/local/lib/plumed" && cd ../../ && tar cf - vim/syntax | tar xf - -C "/construction/science/plumed/stage/usr/local/lib/plumed/" ; fi if test -d ../../vim/help ; then mkdir -p "/construction/science/plumed/stage/usr/local/lib/plumed" && cd ../../ && tar cf - vim/help | tar xf - -C "/construction/science/plumed/stage/usr/local/lib/plumed/" ; fi if test -f ../../vim/scripts.vim ; then mkdir -p "/construction/science/plumed/stage/usr/local/lib/plumed/vim" && cp ../../vim/scripts.vim "/construction/science/plumed/stage/usr/local/lib/plumed/vim/" ; fi chmod -R go+rX,go-w "/construction/science/plumed/stage/usr/local/lib/plumed" chmod -R go+rX,go-w "/construction/science/plumed/stage/usr/local/include/plumed" chmod -R go+rX,go-w "/construction/science/plumed/stage/usr/local/bin/plumed" chmod -R go+rX,go-w "/construction/science/plumed/stage/usr/local/bin/plumed-patch" *** PLUMED has been installed *** WARNING: Staged install with DESTDIR = /construction/science/plumed/stage Install prefix : /usr/local Full name : plumed Setup your environment - Ensure this is in your execution path : /usr/local/bin - Ensure this is in your include path : /usr/local/include - Ensure this is in your library path : /usr/local/lib - Ensure this is in your PKG_CONFIG_PATH path : /usr/local/lib/pkgconfig For runtime binding: - Set this environment variable : PLUMED_KERNEL=/usr/local/lib/libplumedKernel.so To create a tcl module that sets all the variables above, use this one as a starting point: /usr/local/lib/plumed/modulefile To uninstall, remove the following files and directories: /usr/local/lib/plumed /usr/local/share/doc/plumed /usr/local/include/plumed /usr/local/bin/plumed /usr/local/bin/plumed-patch /usr/local/bin/plumed-config /usr/local/lib/pkgconfig/plumed.pc /usr/local/lib/libplumed.so /usr/local/lib/libplumedKernel.so A vim plugin can be found here: /usr/local/lib/plumed/vim/ Copy it to /construction/science/plumed/.vim/ directory Alternatively: - Set this environment variable : PLUMED_VIMPATH=/usr/local/lib/plumed/vim - Add the command 'let &runtimepath.=','.$PLUMED_VIMPATH' to your .vimrc file From vim, you can use :set syntax=plumed to enable it gmake[4]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src/lib' gmake[3]: Leaving directory '/construction/science/plumed/plumed2-2.6.1/src' gmake[2]: Leaving directory '/construction/science/plumed/plumed2-2.6.1' ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:26 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for plumed-2.6.1 file sizes/checksums [510]: 0% file sizes/checksums [510]: 19% file sizes/checksums [510]: 39% file sizes/checksums [510]: 58% file sizes/checksums [510]: 78% file sizes/checksums [510]: 98% file sizes/checksums [510]: 100% packing files [510]: 0% packing files [510]: 19% packing files [510]: 39% packing files [510]: 58% packing files [510]: 78% packing files [510]: 98% packing files [510]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:51 TOTAL TIME 00:07:20